The FireRed & LeafGreen arc starts off with Green about to meet her long-lost parents, but they are sucked into a vortex created by a mysterious Pokémon! Red and Blue want to help, but first they must improve their battle skills. Then, the Three Beasts of Team Rocket are up to their old tricks again!

In the Emerald storyline, Gold and Crystal are back! Professor Oak sends the two friends to help rescue Red, Yellow, Blue and Green—who have all been turned to stone! But first, the pair must fight a fearsome creature that Archie, the former leader of Team Aqua, wished into existence using the powers of the Wish Pokémon Jirachi!